I'm modelling G-protein coupled receptors using rhodopsin as a template.
When I compare the Ramachandran plot of the models vs that of rhodopsin,
the models have much more ideal helices than the rhodopsin X-ray structure
Is this because:
1) The homology is relatively low (20-30%) and the distance constraints
receive a low weight in the pdf function??
2) The helices in rhodopsin are less regular than the globular proteins
used in the pdf parametrization??
3) None of the above...
Dan Thomas Major (at Dr. B. Fischer's lab)